Low-pass nanopore sequencing for measurement of global methylation levels in plants DOI Creative Commons
Yusmiati Liau, Annabel Whibley, Amy M. Hill

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Dec. 23, 2024

Nanopore sequencing enables detection of DNA methylation at the same time as identification canonical sequence. A recent study validated low-pass nanopore to accurately estimate global levels in vertebrates with coverage low 0.01x. We investigated applicability this approach plants by testing three plant species and analysed effect technical biological parameters on precision accuracy. Our results indicate that higher (0.1x) is required achieve accuracy assessing comparable vertebrates. Shorter read length a closer sequence match between sample reference genome improved measurement Application method Vitis vinifera showed consistent across different leaf sizes, preservation extraction methods, whereas varieties tissue types did exhibit differences. Similarly, distinct patterns were observed genomic features. findings suggest suitability low-cost screening tool for validation experimental parameters, developmental courses, assess status modification contexts level whole or abundant features such transposable elements.

Language: Английский

Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch (Betula papyrifera) exposed to nickel DOI
K. K. Nkongolo, M. Paul

Genome, Journal Year: 2024, Volume and Issue: 67(10), P. 351 - 367

Published: Sept. 3, 2024

Research in understanding the role of genetics and epigenetics plant adaptations to environmental stressors such as metals is still its infancy. The objective present study assess effect nickel on DNA methylation level distribution white birch ( Betula papyrifera Marshall) using reduced representation bisulfite sequencing (RRBS). methylated C sites each sample revealed that was much higher CG context varying between 54% 65%, followed by CHG (24%–31.5%), then CHH with rate 3.3% 5.2%. analysis differentially regions (DMR) induced both hypermethylation hypomethylation when compared water. Detailed showed for first time a controls, while potassium triggers nickel. Surprisingly, DMRs 38%–42% were located gene bodies, 20%–24% exon, 19%–20% intron, 16%–17% promoters, 0.03%–0.04% transcription start site. RRBS successful detecting mapping DMR plants exposed

Language: Английский

Citations

0
Testarea metilării: o nouă frontieră în screeningul cancerului de col uterin? DOI Creative Commons

Anca Potecă,

Rina Limani,

Labinota Kondirolli

et al.

Ginecologia ro, Journal Year: 2024, Volume and Issue: 3(45), P. 18 - 18

Published: Jan. 1, 2024

Citations

0
Advances in Forensic Genetics: exploring the potential of long read sequencing DOI
Marcel Rodrigues Ferreira, Thássia Mayra Telles Carratto, Tamara Soledad Frontanilla Recalde

et al.

Forensic Science International Genetics, Journal Year: 2024, Volume and Issue: 74, P. 103156 - 103156

Published: Oct. 10, 2024

Language: Английский

Citations

0
Domestication of ornamental plants: Breeding innovations and molecular breakthroughs to bring wild into limelight DOI
Vipasha Verma,

Megha Katoch,

Payal Kapoor

et al.

South African Journal of Botany, Journal Year: 2024, Volume and Issue: 175, P. 436 - 452

Published: Oct. 25, 2024

Language: Английский

Citations

0
Low-pass nanopore sequencing for measurement of global methylation levels in plants DOI Creative Commons
Yusmiati Liau, Annabel Whibley, Amy M. Hill

et al.

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Dec. 23, 2024

Nanopore sequencing enables detection of DNA methylation at the same time as identification canonical sequence. A recent study validated low-pass nanopore to accurately estimate global levels in vertebrates with coverage low 0.01x. We investigated applicability this approach plants by testing three plant species and analysed effect technical biological parameters on precision accuracy. Our results indicate that higher (0.1x) is required achieve accuracy assessing comparable vertebrates. Shorter read length a closer sequence match between sample reference genome improved measurement Application method Vitis vinifera showed consistent across different leaf sizes, preservation extraction methods, whereas varieties tissue types did exhibit differences. Similarly, distinct patterns were observed genomic features. findings suggest suitability low-cost screening tool for validation experimental parameters, developmental courses, assess status modification contexts level whole or abundant features such transposable elements.

Language: Английский

Citations

0